I have a clay floor and hate it, some places of heavy traffic such as in front of the doors and where they typically jump into the back stall/run in shelter are pretty rutted, and a lot of urine and spilled water can accumulate in these "pockets", not to mention it is unsightly and not that great for the horses to be on, but since their small, and spend usually only the nights in the stable, they should be alright until spring when I can fix the dang pot holes!!
We have rubber mats in the stalls, I think they were just generic, nothing fancy, picked up at Tractor Supply type mats but they are great!! Have yet to wear down in almost 4 years of being under pawing, rearing, kicking, bucking, rolling, peeing, horses. I too agree with Andrea, the closer to fit the better. I think that interlocking mats are best however, they are much smaller so are much easier to manage and move outside to be cleaned, especially when you don't have a helper. I saw an ad in Horse Illustrated magazine a few years ago for some that weigh only 12 pounds/ every four foot interlocking square of rubber mat, definitely something to investigate, I think.
If you have concrete aisle floors, you could always put down a single rubber mat where there is cross ties, grooming areas in front of the stalls (not quite sure what you are thinking of) to give horses extra cushion when standing in case you have a horse standing to dry after a bath or waiting to be saddled or harnessed so, should they have to stand for a longer time, it will cut down on leg fatigue.
Dutch all the way!! Build them so they open into the stall, will keep horses from pushing them open and wandering around the stable and getting into trouble. As well, it will save you valuable aisle space. You could do wire, but I have my stalls, mini/pony sized. The dividers and doors are mini/pony sized, but unscrew should I ever redo the stable, or move, so they aren't permanent, and the horses are happy as they can interact with friends when they are inside and groom, as well as hang their heads over the doors and look around the stable. They seem happiest that way.
I feed using on the ground, using black rubber feed tubs. They are easy to clean and disinfect and aren't permanent so is one less thing for a horse to get caught up on and also saves you a little bit of stall space and some money (I think.)
One last thing, WINDOWS. Lots of windows!! I leave mine open pretty much year round, and even if it is 19- (been there done, that, hope to never go back again) I always have some open, the horses love being able to stick their heads out, watch the wildlife in the forests surrounding our place, and breathe lots of fresh air, and feel the sun on their face.
Best of luck with your new barn building venture!! I'm sure whatever you choose your horses will love it.
Dan.